This script takes the downloaded data from the Australian Living Atlas and NSW Atlas for all specified species with more than the specified minimum number of records, as well as the data from the brut dataset, and produces:
1. a pdf of maps of all species locations (if save.maps == TRUE)
2. a csv file of location points for input into Maxent maxent.data
3. a spp file for input into Zonation that lists all of the species ascii files and other attributes zonation.spp
The first part of the script takes the brut dataset where species have been coded into taxonomic groups and identifies species that have more than the specified minimum number of records that fall within the Hunter region as masked by a shapefile. We extract all records for these species from within the NSW North Coast and Sydney Basin bioregions
Then we run a loop that runs through the species listed as Vulnerable or Endangered under the NSW legislation on the NSW database that have more than the minumim number of records and extracts the latitude and longitude of all records in the ALA and NSW databases.
Note that these records are for the entire time period - this will need to be confined to something more sensible
# load packages and set working directory
rm(list = ls())
packages(ggplot2)
packages(ggmap)
packages(maptools)
packages(sp)
setwd("C:/Users/awhitehead/Documents/GIS data/Hunter/species point data/")
# save the maps as a pdf
save.maps <- TRUE
save.output <- TRUE
combine.records <- function(NC.records, SB.records) {
tryCatch({
rbind(NC.records, SB.records)
}, error = function(err) {
if (is.null(NC.records) == TRUE & is.null(SB.records) == FALSE) {
return(SB.records)
} else if (is.null(SB.records) == TRUE & is.null(NC.records) == FALSE) {
return(NC.records)
} else cat("")
})
}
# set the google map background for the species plots and create
# background map
map <- get_map(location = c(151.25, -32.49), zoom = 6, maptype = "hybrid", color = "bw")
hunter.mask <- readShapePoly("C:/Users/awhitehead/Documents/GIS data/Hunter/data from Brendan/data/variables/projected GDA94/poly_lower_hunter.shp")
hunter.mask.data <- fortify(hunter.mask)
cma.mask <- readShapePoly("C:/Users/awhitehead/Documents/GIS data/Hunter/Plans/HCR_CMA/HCR_CMA_GDA94.shp")
cma.mask.data <- fortify(cma.mask)
ibra.mask <- readShapePoly("C:/Users/awhitehead/Documents/GIS data/Hunter/Plans/Bioregions/hunter_bioregions.shp")
ibra.mask.data <- fortify(ibra.mask)
print(base.map <- ggmap(map) + geom_polygon(aes(x = long, y = lat, group = group),
data = hunter.mask.data, colour = "yellow", fill = "black", alpha = 0.1,
size = 0.3) + geom_polygon(aes(x = long, y = lat, group = group), data = ibra.mask.data,
colour = "light blue", fill = "black", alpha = 0.1, size = 0.3))
# The minimum number of records required for a species to be included
min.records <- 30
# open species list
protected.species <- read.csv("C:/Users/awhitehead/Documents/GIS data/Hunter/species point data/IBRA threatened species list.csv")
threatened.species <- rbind(protected.species[grep("E", protected.species$NSW.status),
], protected.species[grep("V", protected.species$NSW.status), ])
threatened.species <- threatened.species[!duplicated(threatened.species), ]
# identify which species have more than the minimum number of records
# across both atlases
species.list <- threatened.species$Scientific.Name[rowSums(threatened.species[,
c("ALA.records", "NSW.records")], na.rm = TRUE) > min.records]
species.list <- species.list[!is.na(species.list) == TRUE]
# create empty dataframes for the output data
maxent.data <- d(species = NULL, longitude = NULL, latitude = NULL, database = NULL)
atlas.zonation.spp <- d(weight = rep(1, length(species.list)), alpha = 1, bqp.row = 1,
bqp.buffer = 1, cell.removal = 1, species = NA)
missing.NSW.sp <- NULL
setwd("C:/Users/awhitehead/Documents/GIS data/Hunter/species point data/")
# open the brut dataset and generate spatial co-ordinates
modeled.sp <- read.csv("C:/Users/awhitehead/Documents/GIS data/Australia-wide/species data/modeledsp_order_brut.csv")
modeled.sp$database <- "brut"
coordinates(modeled.sp) <- c("Lon_Centre", "Lat_Centre")
# clip the brut data by the CMA mask, provided there are at least 30
# points in the HCCREMS
ibra.sp <- modeled.sp[ibra.mask, ]
hunter.sp <- modeled.sp[hunter.mask, ]
# identify how many observations for each species within the hunter
n.obs <- d(obs = tapply(hunter.sp$SEL, hunter.sp$TAXON_ID, sum))
n.obs$taxa <- rownames(n.obs)
n.obs <- n.obs[n.obs$obs > min.records, ]
brut.zonation.spp <- d(weight = rep(1, nrow(n.obs)), alpha = 1, bqp.row = 1,
bqp.buffer = 1, cell.removal = 1, species = NA)
# set specifications for pdf file if save.maps == TRUE
if (save.maps == TRUE) pdf("species point data maps.pdf", paper = "a4r")
# extract each species with more than the minimum number of records from
# brut dataset
for (i in seq(n.obs$taxa)) {
input <- as.data.frame(ibra.sp[ibra.sp$TAXON_ID == n.obs$taxa[i], ])
colnames(input)[3:4] <- c("latitude", "longitude")
input$species <- paste(input$Ordertot, input$TAXON_ID)
# if(nrow(input) > min.records){
maxent.data <- rbind(maxent.data, input[, c("species", "longitude", "latitude",
"database")])
print(sp.map <- base.map + geom_point(aes(x = longitude, y = latitude, color = species),
data = input, alpha = 0.5))
brut.zonation.spp$species[i] <- glue(unique(input$species), ".asc")
cat("\n", "Adding", nrow(input), "records for", as.character(input$species[i]),
"to maxent data")
# }
}
##
## Adding 303 records for Passeriformes 1422 to maxent data
##
## Adding 312 records for Psittaciformes 2218 to maxent data
##
## Adding 1219 records for Dasyuromorphia 4227 to maxent data
##
## Adding 346 records for Diprotodontia 4395 to maxent data
##
## Adding 1559 records for Chiroptera 4768 to maxent data
##
## Adding 288 records for Chiroptera 4780 to maxent data
##
## Adding 1246 records for Chiroptera 4793 to maxent data
##
## Adding 161 records for Rodentia 4969 to maxent data
##
## Adding 272 records for Salientia 15106 to maxent data
##
## Adding 357 records for Salientia 15107 to maxent data
##
## Adding 112 records for Testudines 15208 to maxent data
##
## Adding 351 records for Salientia 15702 to maxent data
##
## Adding 187 records for Fabales 29616 to maxent data
##
## Adding 101 records for Myrtales 36558 to maxent data
##
## Adding 230 records for Myrtales 40503 to maxent data
##
## Adding 85 records for Asterales 43842 to maxent data
##
## Adding 117 records for Myrtales 45194 to maxent data
##
## Adding 107 records for Myrtales 48189 to maxent data
##
## Adding 218 records for Proteales 48299 to maxent data
# create the zonation.spp file for the brut dataset
brut.zonation.spp <- brut.zonation.spp[!is.na(brut.zonation.spp$species), ]
setwd("C:/Users/awhitehead/Documents/GIS data/Hunter/species point data/")
# run loop to extract data from ALA and NSW atlas data by species
for (i in seq(species.list)) {
# extract ALA data
if (!is.na(threatened.species$Downloaded.ALA[threatened.species$Scientific.Name ==
species.list[i]]) == TRUE) {
ALA.data <- read.csv(glue("ALA data/", species.list[i], ".csv"))
ALA.labels <- c("Latitude...processed", "Longitude...processed")
colnames(ALA.data)[which(names(ALA.data) %in% ALA.labels)] <- c("latitude",
"longitude")
ALA.data$index <- paste(sprintf("%.6f", ALA.data$latitude), sprintf("%.6f",
ALA.data$longitude))
ALA.data$database <- "ALA"
ALA.data$species <- species.list[i]
} else ALA.data <- NULL
# extract NSW Atlas data
if (!is.na(threatened.species$Downloaded.NSW[threatened.species$Scientific.Name ==
species.list[i]]) == TRUE) {
NSW.data <- read.csv(glue("NSW Atlas data/", species.list[i], ".csv"))
colnames(NSW.data)[c(21:22)] <- c("latitude", "longitude")
NSW.data$index <- paste(sprintf("%.6f", NSW.data$latitude), sprintf("%.6f",
NSW.data$longitude))
NSW.data$database <- "NSW"
NSW.data$species <- species.list[i]
} else NSW.data <- NULL
ALA.NSW.data <- combine.records(ALA.data[, c("species", "longitude", "latitude",
"database")], NSW.data[, c("species", "longitude", "latitude", "database")])
# only include species if more than the minimum number of records occur in
# the HCCREMS area
ALA.NSW.points <- SpatialPoints(ALA.NSW.data[, c("longitude", "latitude")])
in.hunter <- nrow(d(ALA.NSW.points[complete.cases(over(ALA.NSW.points, hunter.mask)),
]))
# produce maps of the distribution of each species
if (in.hunter > min.records) {
print(sp.map <- base.map + geom_point(aes(x = longitude, y = latitude,
color = database, shape = species), data = ALA.NSW.data, alpha = 0.5))
# output data for maxent analyses
maxent.data <- rbind(maxent.data, ALA.NSW.data)
cat("\n", "Adding", nrow(ALA.NSW.data), "records for", as.character(species.list[i]),
"to maxent data", "\n")
# create file for zonation analyses
atlas.zonation.spp$species[i] <- glue(species.list[i], ".asc")
}
# remove all species-specific datafiles, so they don't mess up the next
# round of the loop
suppressWarnings(rm(ALA.data, NSW.data, ALA.NSW.data, ALA.NSW.points, in.hunter))
gc()
}
##
## Adding 2275 records for Mixophyes balbus to maxent data
##
## Adding 1641 records for Mixophyes iteratus to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 17973 records for Litoria aurea to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 1396 records for Petrogale penicillata to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 1308 records for Acacia bynoeana to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 39 records for Eucalyptus castrensis to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 532 records for Syzygium paniculatum to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 749 records for Zieria smithii to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 56 records for Zannichellia palustris to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 1256 records for Hibbertia procumbens to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 246 records for Acacia prominens to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 212 records for Prostanthera askania to maxent data
##
## Adding 933 records for Prostanthera junonis to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 260 records for Eucalyptus oblonga to maxent data
##
## Adding 217 records for Eucalyptus parramattensis subsp. parramattensis to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 86 records for Diuris bracteata to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 1264 records for Crinia tinnula to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 3346 records for Pseudophryne australis to maxent data
##
## Adding 288 records for Litoria brevipalmata to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 410 records for Chelonia mydas to maxent data
##
## Adding 341 records for Hoplocephalus stephensii to maxent data
##
## Adding 7133 records for Dasyurus maculatus to maxent data
##
## Adding 989 records for Phascogale tapoatafa to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 32865 records for Phascolarctos cinereus to maxent data
##
## Adding 972 records for Cercartetus nanus to maxent data
##
## Adding 12653 records for Petaurus australis to maxent data
##
## Adding 2595 records for Petaurus norfolcensis to maxent data
##
## Adding 634 records for Potorous tridactylus to maxent data
##
## Adding 1009 records for Macropus parma to maxent data
##
## Adding 14167 records for Pteropus poliocephalus to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 221 records for Saccolaimus flaviventris to maxent data
##
## Adding 1870 records for Mormopterus norfolkensis to maxent data
##
## Adding 810 records for Chalinolobus dwyeri to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 1556 records for Falsistrellus tasmaniensis to maxent data
##
## Adding 1170 records for Kerivoula papuensis to maxent data
##
## Adding 4045 records for Miniopterus australis to maxent data
##
## Adding 4338 records for Miniopterus schreibersii oceanensis to maxent data
##
## Adding 5720 records for Myotis macropus to maxent data
##
## Adding 1561 records for Scoteanax rueppellii to maxent data
##
## Adding 198 records for Vespadelus troughtoni to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 2341 records for Rutidosis heterogama to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 4845 records for Tetratheca juncea to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 157 records for Maundia triglochinoides to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 188 records for Prostanthera densa to maxent data
##
## Adding 1915 records for Angophora inopina to maxent data
##
## Adding 2384 records for Callistemon linearifolius to maxent data
##
## Adding 492 records for Eucalyptus camfieldii to maxent data
##
## Adding 833 records for Eucalyptus glaucina to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 2328 records for Eucalyptus parramattensis subsp. decadens to maxent data
##
## Adding 86 records for Eucalyptus pumila to maxent data
##
## Adding 2149 records for Melaleuca biconvexa to maxent data
##
## Adding 220 records for Melaleuca groveana to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 347 records for Cryptostylis hunteriana to maxent data
##
## Adding 104 records for Diuris praecox to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 1455 records for Heleioporus australiacus to maxent data
##
## Adding 944 records for Litoria littlejohni to maxent data
##
## Adding 489 records for Varanus rosenbergi to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 361 records for Astrotricha crassifolia to maxent data
##
## Adding 161 records for Olearia cordata to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 2132 records for Tetratheca glandulosa to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 667 records for Darwinia glaucophylla to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
##
## Adding 84 records for Grevillea shiressii to maxent data
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
## Warning: no non-missing arguments to min; returning Inf
## Warning: no non-missing arguments to max; returning -Inf
zonation.spp <- rbind(brut.zonation.spp, atlas.zonation.spp)
# close pdf file
if (save.maps == TRUE) dev.off()
## pdf
## 3
# print sample map for RMarkdown
print(sp.map)
These are combined together in maxent.data where there are 161587 records for
Error in eval(expr, envir, enclos) : object 'n.species' not found
species. Note that there may be duplicate records in these files but they should be filtered out by Maxent. A map of the distribution of each species is saved in a pdf file (C:/Users/awhitehead/Documents/GIS data/Hunter/species point data/species point data maps.pdf)
h(maxent.data)
## species longitude latitude database
## 1 Passeriformes 1422 149.8 -32.41 brut
## 2 Passeriformes 1422 149.8 -32.41 brut
## 3 Passeriformes 1422 149.8 -32.42 brut
## 4 Passeriformes 1422 149.8 -32.41 brut
## 5 Passeriformes 1422 149.8 -32.41 brut
## 6 Passeriformes 1422 149.8 -32.41 brut
if (save.output == TRUE) write.csv(maxent.data, "C:/Users/awhitehead/Documents/GIS data/Hunter/species point data/maxent data/maxent.data.csv",
row.names = FALSE)
The zonation.spp table lists each species and the required input for zonation. These are currently all set to 1 and will require some tinkering as we get further down the line. This assumes that we will run all the listed species in Maxent from maxent.data.csv, creating all the relevant ascii files. Or we will use this same data in biomod2.
h(zonation.spp)
## weight alpha bqp.row bqp.buffer cell.removal species
## 1 1 1 1 1 1 Passeriformes 1422.asc
## 2 1 1 1 1 1 Psittaciformes 2218.asc
## 3 1 1 1 1 1 Dasyuromorphia 4227.asc
## 4 1 1 1 1 1 Diprotodontia 4395.asc
## 5 1 1 1 1 1 Chiroptera 4768.asc
## 6 1 1 1 1 1 Chiroptera 4780.asc
if (save.output == TRUE) write.table(zonation.spp, glue("C:/Users/awhitehead/Documents/GIS data/Hunter/species point data/maxent data/zonation.spp.txt"),
sep = "\t", row.names = FALSE, col.names = FALSE)
This file was last updated on 4 March 2013 and last run on 04 March 2013.